00001 /********************************************************************** 00002 parsmart.h - Daylight SMARTS parser. 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison 00006 00007 This file is part of the Open Babel project. 00008 For more information, see <http://openbabel.sourceforge.net/> 00009 00010 This program is free software; you can redistribute it and/or modify 00011 it under the terms of the GNU General Public License as published by 00012 the Free Software Foundation version 2 of the License. 00013 00014 This program is distributed in the hope that it will be useful, 00015 but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00017 GNU General Public License for more details. 00018 ***********************************************************************/ 00019 00020 #ifndef OB_PARSMART_H 00021 #define OB_PARSMART_H 00022 00023 #include <string> 00024 #include <vector> 00025 00026 #include <openbabel/mol.h> 00027 00028 /*==========================*/ 00029 /* SMARTS Data Structures */ 00030 /*==========================*/ 00031 00032 namespace OpenBabel 00033 { 00034 00035 // mark this so that SWIG will not attempt to wrap for scripting languages 00036 00037 #ifndef SWIG 00038 00041 typedef union _AtomExpr { 00042 int type; 00043 struct 00044 { 00045 int type; 00046 int prop; 00047 int value; 00048 } 00049 leaf; 00050 struct 00051 { 00052 int type; 00053 void *recur; 00054 } 00055 recur; 00056 struct 00057 { 00058 int type; 00059 union _AtomExpr *arg; 00060 } 00061 mon; 00062 struct 00063 { 00064 int type; 00065 union _AtomExpr *lft; 00066 union _AtomExpr *rgt; 00067 } 00068 bin; 00069 } AtomExpr; 00070 00071 #define BE_LEAF 0x01 00072 #define BE_ANDHI 0x02 00073 #define BE_ANDLO 0x03 00074 #define BE_NOT 0x04 00075 #define BE_OR 0x05 00076 00077 #define BL_CONST 0x01 00078 #define BL_TYPE 0x02 00079 00080 #define BT_SINGLE 0x01 00081 #define BT_DOUBLE 0x02 00082 #define BT_TRIPLE 0x03 00083 #define BT_AROM 0x04 00084 #define BT_UP 0x05 00085 #define BT_DOWN 0x06 00086 #define BT_UPUNSPEC 0x07 00087 #define BT_DOWNUNSPEC 0x08 00088 #define BT_RING 0x09 00089 00092 typedef union _BondExpr { 00093 int type; 00094 struct 00095 { 00096 int type; 00097 int prop; 00098 int value; 00099 } 00100 leaf; 00101 struct 00102 { 00103 int type; 00104 union _BondExpr *arg; 00105 } 00106 mon; 00107 struct 00108 { 00109 int type; 00110 union _BondExpr *lft; 00111 union _BondExpr *rgt; 00112 } 00113 bin; 00114 } BondExpr; 00115 00118 typedef struct 00119 { 00120 BondExpr *expr; 00121 int src,dst; 00122 int visit; 00123 bool grow; 00124 } 00125 BondSpec; 00126 00129 typedef struct 00130 { 00131 AtomExpr *expr; 00132 int visit; 00133 int part; 00134 int chiral_flag; 00135 int vb; 00136 } 00137 AtomSpec; 00138 00141 typedef struct 00142 { 00143 int aalloc,acount; 00144 int balloc,bcount; 00145 bool ischiral; 00146 AtomSpec *atom; 00147 BondSpec *bond; 00148 int parts; 00149 } 00150 Pattern; 00151 #else 00152 // for SWIG, just forward declare that we have some Pattern struct 00153 // (but this is private and not wrapped for scripting languages) 00154 struct Pattern; 00155 #endif 00156 00157 // class introduction in parsmart.cpp 00159 class OBAPI OBSmartsPattern 00160 { 00161 protected: 00162 std::vector<bool> _growbond; 00163 std::vector<std::vector<int> > _mlist; 00164 Pattern *_pat; 00165 std::string _str; 00166 00167 public: 00168 OBSmartsPattern() : _pat(NULL) { } 00169 virtual ~OBSmartsPattern(); 00170 00171 OBSmartsPattern(const OBSmartsPattern& cp): _pat(NULL) 00172 { 00173 *this = cp; 00174 } 00175 OBSmartsPattern& operator=(const OBSmartsPattern& cp) 00176 { 00177 if (_pat) 00178 delete [] _pat; 00179 _pat = NULL; 00180 std::string s = cp._str; 00181 Init(s); 00182 return (*this); 00183 } 00184 00186 00187 00188 00189 bool Init(const char* pattern); 00192 bool Init(const std::string& pattern); 00194 00196 00197 00198 const std::string &GetSMARTS() const { return _str; } 00200 std::string &GetSMARTS() { return _str; } 00201 00203 bool Empty() const { return(_pat == NULL); } 00205 bool IsValid() const { return(_pat != NULL); } 00206 00208 unsigned int NumAtoms() const 00209 { 00210 return _pat ? _pat->acount : 0; 00211 } 00213 unsigned int NumBonds() const 00214 { 00215 return _pat ? _pat->bcount : 0; 00216 } 00217 00223 void GetBond(int& src,int& dst,int& ord,int idx); 00225 int GetAtomicNum(int idx); 00227 int GetCharge(int idx); 00228 00230 int GetVectorBinding(int idx) const 00231 { 00232 return(_pat->atom[idx].vb); 00233 } 00235 00237 00238 00239 00240 00241 00242 bool Match(OBMol &mol, bool single=false); 00243 00244 bool RestrictedMatch(OBMol &mol, std::vector<std::pair<int,int> > &pairs, bool single=false); 00245 00246 bool RestrictedMatch(OBMol &mol, OBBitVec &bv, bool single=false); 00249 unsigned int NumMatches() const 00250 { 00251 return (unsigned int)_mlist.size(); 00252 } 00253 00256 std::vector<std::vector<int> > &GetMapList() 00257 { 00258 return(_mlist); 00259 } 00261 std::vector<std::vector<int> >::iterator BeginMList() 00262 { 00263 return(_mlist.begin()); 00264 } 00266 std::vector<std::vector<int> >::iterator EndMList() 00267 { 00268 return(_mlist.end()); 00269 } 00270 00272 00282 std::vector<std::vector<int> > &GetUMapList(); 00284 00286 void WriteMapList(std::ostream&); 00287 }; 00288 00292 class OBAPI OBSSMatch 00293 { 00294 protected: 00295 bool *_uatoms; 00296 OBMol *_mol; 00297 Pattern *_pat; 00298 std::vector<int> _map; 00299 00300 public: 00301 OBSSMatch(OBMol&,Pattern*); 00302 ~OBSSMatch(); 00303 void Match(std::vector<std::vector<int> > &v, int bidx=-1); 00304 }; 00305 00306 OBAPI void SmartsLexReplace(std::string &, 00307 std::vector<std::pair<std::string,std::string> > &); 00308 00309 } // end namespace OpenBabel 00310 00311 #endif // OB_PARSMART_H 00312
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.